Silver noble metal nanoparticles that are<10 nm often possess multiply twinned grains allowing them to adopt shapes and atomic structures not observed in bulk materials. The properties exhibited by particles with multiply twinned polycrystalline structures are often far different from those of single-crystalline particles and from the bulk. I will present experimental evidence that silver nanoparticles<10 nm undergo a reversible structural transformation under hydrostatic pressures up to 10 GPa. Results for nanoparticles in the intermediate size range of 5 to 10 nm suggest a reversible linear pressure-dependent rhombohedral distortion which has not been previously observed in bulk silver. I propose a mechanism for this transitiion that considers the bond-length distribution in idealized multiply twinned icosahedral particles. Results for nanoparticles of 3.9 nm suggest a reversible linear pressure-dependent orthorhombic distortion. This distortion is interpreted in the context of idealized decahedral particles. In addition, given these size-dependent measurements of silver nanoparticle compression with pressure, we have constructed a pressure calibration curve. Encapsulating these silver nanoparticles in hollow metal oxide nanospheres then allows us to measure the pressure inside a nanoshell using x-ray diffraction. We demonstrate the measurement of pressure gradients across nanoshells and show that these nanoshells have maximum resolved shear strengths …

The purpose of this research was to expand the chemiluminescence microscopy applications in live bacterial/mammalian cell imaging and to improve the detection sensitivity for ATP leaking or release events. We first demonstrated that chemiluminescence (CL) imaging can be used to interrogate single bacterial cells. While using a luminometer allows detecting ATP from cell lysate extracted from at least 10 bacterial cells, all previous cell CL detection never reached this sensitivity of single bacteria level. We approached this goal with a different strategy from before: instead of breaking bacterial cell membrane and trying to capture the transiently diluted ATP with the firefly luciferase CL assay, we introduced the firefly luciferase enzyme into bacteria using the modern genetic techniques and placed the CL reaction substrate D-luciferin outside the cells. By damaging the cell membrane with various antibacterial drugs including antibiotics such as Penicillins and bacteriophages, the D-luciferin molecules diffused inside the cell and initiated the reaction that produces CL light. As firefly luciferases are large protein molecules which are retained within the cells before the total rupture and intracellular ATP concentration is high at the millmolar level, the CL reaction of firefly luciferase, ATP and D-luciferin can be kept for a relatively …

One and two dimensional time-resolved vibrational spectroscopy has been used to investigate the elementary reactions of several prototypical organometallic complexes in room temperature solution. The electron transfer and ligand substitution reactions of photogenerated 17-electron organometallic radicals CpW(CO){sub 3} and CpFe(CO){sub 2} have been examined with one dimensional spectroscopy on the picosecond through microsecond time-scales, revealing the importance of caging effects and odd-electron intermediates in these reactions. Similarly, an investigation of the photophysics of the simple Fischer carbene complex Cr(CO){sub 5}[CMe(OMe)] showed that this class of molecule undergoes an unusual molecular rearrangement on the picosecond time-scale, briefly forming a metal-ketene complex. Although time-resolved spectroscopy has long been used for these types of photoinitiated reactions, the advent of two dimensional vibrational spectroscopy (2D-IR) opens the possibility to examine the ultrafast dynamics of molecules under thermal equilibrium conditions. Using this method, the picosecond fluxional rearrangements of the model metal carbonyl Fe(CO){sub 5} have been examined, revealing the mechanism, time-scale, and transition state of the fluxional reaction. The success of this experiment demonstrates that 2D-IR is a powerful technique to examine the thermally-driven, ultrafast rearrangements of organometallic molecules in solution.

This work presents simultaneous branching fraction measurements of the decay modes {tau}{sup -} {yields} K{sup -} n{pi}{sup 0}{nu}{sub {tau}} with n = 0,1,2,3 and {tau}{sup -} {yields} {pi}{sup -} n{pi}{sup 0}{nu}{sub {tau}} with n = 3,4. The analysis is based on a data sample of 427 x 10{sup 6} {tau}{sup +}{tau}{sup -} pairs recorded with the BABAR detector, which corresponds to an integrated luminosity of 464.4 fb{sup -1}. The measured values are {Beta}({tau}{sup -} {yields} K{sup -}{nu}{sub {tau}}) = (6.57 {+-} 0.03 {+-} 0.11) x 10{sup -3}, {Beta}({tau}{sup -} {yields} K{sup -}{pi}{sup 0}{nu}{sub {tau}}) = (4.61 {+-} 0.03 {+-} 0.11) x 10{sup -3}, {Beta}({tau}{sup -} {yields} K{sup -} {pi}{sup 0}{pi}{sup 0}{nu}{sub {tau}}) = (5.05 {+-} 0.17 {+-} 0.44) x 10{sup -4}, {Beta}({tau}{sup -} {yields} K{sup -}{pi}{sup 0}{pi}{sup 0}{pi}{sup 0}{nu}{sub {tau}}) = (1.31 {+-} 0.43 {+-} 0.40) x 10{sup -4}, {Beta}({tau}{sup 0} {yields} {pi}{sup 0}{pi}{sup 0}{pi}{sup 0}{pi}{sup 0}{nu}{sub {tau}}) = (1.263 {+-} 0.008 {+-} 0.078) x 10{sup -2} and {Beta}({tau}{sup 0} {yields} {pi}{sup 0}{pi}{sup 0}{pi}{sup 0}{pi}{sup 0}{pi}{sup 0}{nu}{sub {tau}}) = (9.6 {+-} 0.5 {+-} 1.2) x 10{sup -4}, where the uncertainties are statistical and systematic, respectively. All measurements are compatible with the current world averages whereas the uncertainties are significantly smaller …

Optimization techniques are finding their inroads into the field of nuclear physics calculations where the objective functions are very complex and computationally intensive. A vast space of parameters needs searching to obtain a good match between theoretical (computed) and experimental observables, such as energy levels and spectra. Manual calculation defies the scope of such complex calculation and are prone to error at the same time. This body of work attempts to formulate a design and implement it which would integrate the ab initio nuclear physics code MFDn and the VTDIRECT95 code. VTDIRECT95 is a Fortran95 suite of parallel code implementing the derivative-free optimization algorithm DIRECT. Proposed design is implemented for a serial and parallel version of the optimization technique. Experiment with the initial implementation of the design showing good matches for several single-nucleus cases are conducted. Determination and assignment of appropriate number of processors for parallel integration code is implemented to increase the efficiency and resource utilization in the case of multiple nuclei parameter search.

Understanding chemical reactions requires the knowledge of the elementary steps of breaking and making bonds, and often a variety of experimental techniques are needed to achieve this goal. The initial steps occur on the femto- through picosecond time-scales, requiring the use of ultrafast spectroscopic methods, while the rate-limiting steps often occur more slowly, requiring alternative techniques. Ultrafast one and two-dimensional infrared and step-scan FTIR spectroscopies are used to investigate the photochemical reactions of four organometallic complexes. The analysis leads to a detailed understanding of mechanisms that are general in nature and may be applicable to a variety of reactions.

The field of spintronics offers perspectives for seamless integration of coupled and inter-tunable electrical and magnetic properties in a single device. For integration of the spin degree of freedom with current electronic technology, new semiconductors are needed that show electrically-tunable magnetic properties at room temperature and above. Dilute magnetic semiconductors derived from III-V compounds, like GaMnAs and InMnAs, show coupled and tunable magnetic, transport, and optical properties, due to the fact that their ferromagnetism is hole-mediated. These unconventional materials are ideal systems for manipulating the magnetic order by changing the carrier polarization, population density, and energy band distribution of the complementary subsystem of holes. This is the main theme we cover in this thesis. In particular, we develop a unique setup by use of ultraviolet pump, near-infrared probe femtosecond laser pulses, that allows for magneto-optical Kerr effect (MOKE) spectroscopy experiments. We photo-excite transient carriers in our samples, and measure the induced transient magnetization dynamics. One set of experiments performed allowed us to observe for the first time enhancement of the ferromagnetic order in GaMnAs, on an ultrafast time scale of hundreds of picoseconds. The corresponding transient increase of Curie temperature (Tc, the temperature above which a ferromagnetic material loses its …

The search for the fundamental constituents of matter has been pursued and studied since the dawn of civilization. As early as the fourth century BCE, Democritus, expanding the teachings of Leucippus, proposed small, indivisible entities called atoms, interacting with each other to form the Universe. Democritus was convinced of this by observing the environment around him. He observed, for example, how a collection of tiny grains of sand can make out smooth beaches. Today, following the lead set by Democritus more than 2500 years ago, at the heart of particle physics is the hypothesis that everything we can observe in the Universe is made of a small number of fundamental particles interacting with each other. In contrast to Democritus, for the last hundred years we have been able to perform experiments that probe deeper and deeper into matter in the search for the fundamental particles of nature. Today's knowledge is encapsulated in the Standard Model of particle physics, a model describing the fundamental particles and their interactions. It is within this model that the work in this thesis is presented. This work attempts to add to the understanding of the Standard Model by measuring the relative branching fraction of the …

Three major high performance quantum chemistry computational packages, NWChem, GAMESS and MPQC have been developed by different research efforts following different design patterns. The goal is to achieve interoperability among these packages by overcoming the challenges caused by the different communication patterns and software design of each of these packages. A chemistry algorithm is hard to develop as well as being a time consuming process; integration of large quantum chemistry packages will allow resource sharing and thus avoid reinvention of the wheel. Creating connections between these incompatible packages is the major motivation of the proposed work. This interoperability is achieved by bringing the benefits of Component Based Software Engineering through a plug-and-play component framework called Common Component Architecture (CCA). In this thesis, I present a strategy and process used for interfacing two widely used and important computational chemistry methodologies: Quantum Mechanics and Molecular Mechanics. To show the feasibility of the proposed approach the Tuning and Analysis Utility (TAU) has been coupled with NWChem code and its CCA components. Results show that the overhead is negligible when compared to the ease and potential of organizing and coping with large-scale software applications.

Aptamers are short single-stranded nucleic acids that can bind to their targets with high specificity and high affinity. To study aptamer function and dynamics, the malachite green aptamer was chosen as a model. Malachite green (MG) bleaching, in which an OH- attacks the central carbon (C1) of MG, was inhibited in the presence of the malachite green aptamer (MGA). The inhibition of MG bleaching by MGA could be reversed by an antisense oligonucleotide (AS) complementary to the MGA binding pocket. Computational cavity analysis of the NMR structure of the MGA-MG complex predicted that the OH{sup -} is sterically excluded from the C1 of MG. The prediction was confirmed experimentally using variants of the MGA with changes in the MG binding pocket. This work shows that molecular reactivity can be reversibly regulated by an aptamer-AS pair based on steric hindrance. In addition to demonstrate that aptamers could control molecular reactivity, aptamer dynamics was studied with a strategy combining molecular dynamics (MD) simulation and experimental verification. MD simulation predicted that the MG binding pocket of the MGA is largely pre-organized and that binding of MG involves reorganization of the pocket and a simultaneous twisting of the MGA terminal stems around the pocket. …

The Standard Model (SM) of particle physics successfully describes all of the observed interactions of the fundamental particles (with the exception of non-zero neutrino mass). Despite this enormous success, the SM is widely viewed as an incomplete theory. For example, the size of the asymmetry between matter and antimatter is not nearly large enough to account for the abundance of matter observed throughout the universe. It is thus believed that as-yet-unknown physical phenomena must exist that introduce new asymmetries between matter and antimatter. In this thesis, by studying decays that happen only rarely in the SM, we make measurements of asymmetries between matter and antimatter that are potentially sensitive to the existence of processes beyond the SM. At the PEP-II asymmetric-energy B Factory at SLAC, electrons and positrons are collided at the {Upsilon}(4S) resonance to create pairs of B mesons. The BABAR detector is used to measure the subsequent decay products. Using 383 million {Upsilon}(4S) {yields} B{bar B} decays, we study the decay B{sup 0} {yields} K{sup +}K{sup -}K{sup 0}. In the SM, this decay is dominated by loop amplitudes. Asymmetries between matter and antimatter (CP asymmetries) are extracted by measuring the time-dependence of the complex amplitudes describing the B{sup …

This thesis describes the measurement of the direct CP violation in the b {yields} sc{bar c} transition using the decay B{sup +} {yields} J/{psi}K{sup +}, and in the b {yields} dc{bar c} transition using the decay B{sup +} {yields} J/{psi}{pi}{sup +}. The decays of B{sup +} mesons are reconstructed in approximately 2.8 fb{sup -1} of data recorded by D0 detector in 2002-2007 during Run II of Fermilab Tevatron collider. Using the unbinned likelihood fit, a signal of 40,222 {+-} 242 of B{sup +} {yields} J/{psi}K{sup +} and 1,578 {+-} 119 of B{sup +} {yields} J/{psi}{pi}{sup +} events is obtained. The corresponding direct CP violation asymmetries are measured to be A{sub CP}(B{sup +} {yields} J/{psi}(1S)K{sup +}) = +0.0077 {+-} 0.0061(stat.) {+-} 0.0027(syst.), and A{sub CP}(B{sup +} {yields} J/{psi}(1S){pi}{sup +}) = - 0.089 {+-} 0.081(stat.) {+-} 0.028(syst.). The result on A{sub CP} (B{sup +} {yields} J/{psi}(1S)K{sup +}) is consistent with the 2007 world average and is the most precise measurement of this asymmetry, with uncertainty approaching the level of the Standard Model prediction. The result on A{sub CP} (B{sup +} {yields} J/{psi}(1S){pi}{sup +}) constitutes the first measurement of this asymmetry at the hadron collider, with uncertainty at the level of the 2007 …

The Mini-Booster neutrino experiment (MiniBooNE) at Fermi National Accelerator Laboratory (Fermilab) is designed to search for {nu}{sub {mu}} {yields} {nu}{sub e} appearance neutrino oscillations. Muon neutrino charged-current quasi-elastic (CCQE) interactions ({nu}{sub {mu}} + n {yields} {mu} + p) make up roughly 40% of our data sample, and it is used to constrain the background and cross sections for the oscillation analysis. Using high-statistics MiniBooNE CCQE data, the muon-neutrino CCQE cross section is measured. The nuclear model is tuned precisely using the MiniBooNE data. The measured total cross section is {sigma} = (1.058 {+-} 0.003 (stat) {+-} 0.111 (syst)) x 10{sup -38} cm{sup 2} at the MiniBooNE muon neutrino beam energy (700-800 MeV). {nu}{sub e} appearance candidate data is also used to search for Lorentz violation. Lorentz symmetry is one of the most fundamental symmetries in modern physics. Neutrino oscillations offer a new method to test it. We found that the MiniBooNE result is not well-described using Lorentz violation, however further investigation is required for a more conclusive result.

The top quark, discovered in 1995 by the CDF and D0 experiments at the Fermilab Tevatron Collider, is the heaviest known fundamental particle. The precise knowledge of its mass yields important constraints on the mass of the yet-unobserved Higgs boson and allows to probe for physics beyond the Standard Model. The first measurement of the top quark mass in the dilepton channel with the Matrix Element method at the D0 experiment is presented. After a short description of the experimental environment and the reconstruction chain from hits in the detector to physical objects, a detailed review of the Matrix Element method is given. The Matrix Element method is based on the likelihood to observe a given event under the assumption of the quantity to be measured, e.g. the mass of the top quark. The method has undergone significant modifications and improvements compared to previous measurements in the lepton+jets channel: the two undetected neutrinos require a new reconstruction scheme for the four-momenta of the final state particles, the small event sample demands the modeling of additional jets in the signal likelihood, and a new likelihood is designed to account for the main source of background containing tauonic Z decay. The Matrix …

Superconducting cavity resonators offer the advantage of high field intensity for a given input power, making them an attractive contender for particle accelerator applications. Power coupling into a superconducting cavity employed in a particle accelerator requires unique provisions to maintain high vacuum and cryogenic temperature on the cavity side, while operating with ambient conditions on the source side. Components introduced to fulfill mechanical requirements must show negligible obstruction of the propagation of the microwave with absence of critical locations that may give rise to electron multipaction, leading to a multiple section design, instead of an aperture, a probe, or a loop structure as found in conventional cavities. A coaxial power coupler for a superconducting multiple-cell cavity at 3.9 GHz has been developed. The cavity is intended to be employed as an accelerator to provide enhanced electron beam quality in a free-electron laser in Hamburg (FLASH) user facility. The design of the coupler called for two windows to sustain high vacuum in the cavity and two bellows to accommodate mechanical dimensional changes resulting from cryogenics. Suppression of multipacting was accomplished by the choice of conductor dimensions and materials with low second yield coefficients. Prior to integration with the cavity, the coupler …

The electronic spin degree of freedom is of general fundamental importance to all matter. Understanding its complex roles and behavior in the solid state, particularly in highly correlated and magnetic materials, has grown increasingly desirable as technology demands advanced devices and materials based on ever stricter comprehension and control of the electron spin. However, direct and efficient spin dependent probes of electronic structure are currently lacking. Angle Resolved Photoemission Spectroscopy (ARPES) has become one of the most successful experimental tools for elucidating solid state electronic structures, bolstered by-continual breakthroughs in efficient instrumentation. In contrast, spin-resolved photoemission spectroscopy has lagged behind due to a lack of similar instrumental advances. The power of photoemission spectroscopy and the pertinence of electronic spin in the current research climate combine to make breakthroughs in Spin and Angle Resolved Photoemission Spectroscopy (SARPES) a high priority . This thesis details the development of a unique instrument for efficient SARPES and represents a radical departure from conventional methods. A custom designed spin polarimeter based on low energy exchange scattering is developed, with projected efficiency gains of two orders of magnitude over current state-of-the-art polarimeters. For energy analysis, the popular hemispherical analyzer is eschewed for a custom Time-of-Flight (TOF) …

A novel repair agent for resin-injection repair of advanced high temperature composites was developed and characterized. The repair agent was based on bisphenol E cyanate ester (BECy) and reinforced with alumina nanoparticles. To ensure good dispersion and compatibility with the BECy matrix in nanocomposites, the alumina nanoparticles were functionalized with silanes. The BECy nanocomposites, containing bare and functionalized alumina nanoparticles, were prepared and evaluated for their thermal, mechanical, rheological, and viscoelastic properties. The monomer of BECy has an extremely low viscosity at ambient temperature, which is good for processability. The cured BECy polymer is a highly cross-linked network with excellent thermal mechanical properties, with a high glass transition temperature (T{sub g}) of 270 C and decomposition temperature above 350 C. The incorporation of alumina nanoparticles enhances the mechanical and rheological properties of the BECy nanocomposites. Additionally, the alumina nanoparticles are shown to catalyze the cure of BECy. Characterization of the nanocomposites included dynamic mechanical analysis, differential scanning calorimetry, thermogravimetric analysis, rheological and rheokinetic evaluation, and transmission electron microscopy. The experimental results show that the BECy nanocomposite is a good candidate as repair agent for resin-injection repair applications.

The present work in this dissertation mainly focuses on the clean fivefold surfaces of i-Al-Pd-Mn quasicrystals as well as the nucleation and growth of Ag films on these surfaces. In addition, Ag film growth on NiAl(110) has been explored in the frame of this dissertation. First, we have investigated the equilibration of a fivefold surface of icosahedral Al-Pd-Mn quasicrystal at 900-915 K and 925-950 K, using Omicron variable temperature scanning tunneling microscope (STM). Annealing at low temperatures resulted in many voids on some terraces while the others were almost void-free. After annealing at 925-950K, void-rich terraces became much rarer. Our STM images suggest that through growth and coalescence of the voids, a different termination becomes exposed on host terraces. All of these observations in our study indicate that even after the quasicrystalline terrace-step structure appears, it evolves with time and temperature. More specifically, based on the STM observations, we conclude that during the annealing a wide range of energetically similar layers nucleate as surface terminations, however, with increasing temperature (and time) this distribution gets narrower via elimination of the metastable void-rich terraces. Next, we have examined the bulk structural models of icosahedral Al-Pd-Mn quasicrystal in terms of the densities, compositions …

The CDF experiment, which uses p{bar p} collisions at {radical}s = 1.9 TeV produced at the Fermilab Tevatron, is unique in its ability to observe all flavors of B hadrons and measure their properties. Among them, CP violation is of fundamental interest. In the B{sup +} and B{sup 0} systems, measurements of CP violation parameters performed essentially at B factories have borne out the predictions of CKM model. Little is known, experimentally, about CP violation in the B{sub s}{sup 0} system. The standard model predicts very little CP violation there, thus any nonzero measurement could be an indication of new physics. In this thesis, we will report on the very first flavor-tagged analysis of approximately 2000 B{sub s}{sup 0} {yields} J/{psi}{phi} decays reconstructed in a 1.35 fb{sup -1} data sample collected at CDF. This channel is sensitive not only to the width difference {Delta}{Lambda} in the B{sub s}{sup 0} system but also to the CP violation parameter {beta}{sub s}. The final result we obtain is a confidence region in the two dimensional space of {beta}{sub s} and {Delta}{Lambda}. Assuming the standard model predictions of {beta}{sub s} and {Delta}{Lambda}, the probability is 15%, corresponding to 1.5 Gaussian standard deviations.

This dissertation presents a search for large extra dimensions in the single photon plus missing transverse energy final states. We use a data sample of approximately 2.7 fb{sup -1} of p{bar p} collisions at {radical}s = 1.96 TeV (recorded with the D{sup -} detector) to investigate direct Kaluza Klein graviton production and set limits, at the 95% C.L., on the fundamental mass scale M{sub D} from 970 GeV to 816 GeV for two to eight extra dimensions.

We report results from a search for neutral Higgs bosons decaying to tau pairs produced in association with a b-quark in 1.6 fb{sup -1} of data taken from June 2006 to March 2008 with the D0 detector at Fermi National Accelerator Laboratory. The final state includes a muon, hadronically decaying tau, and jet identified as coming from a b-quark. We set cross section times branching ratio limits on production of such neutral Higgs bosons {phi} in the mass range from 90 GeV to 160 GeV. Exclusion limits are set at the 95% Confidence Level for several supersymmetric scenarios.

I describe a search for anomalous production of Z pairs through a new massive resonance X in 2.5-2.9 fb{sup -1} of p{bar p} collisions at {radical}s = 1.96 TeV using the CDFII Detector at the Fermilab Tevatron. I reconstruct Z pairs through their decays to electrons, muons, and quarks. To achieve perhaps the most efficient lepton reconstruction ever used at CDF, I apply a thorough understanding of the detector and new reconstruction software heavily revised for this purpose. In particular, I have designed and employ new general-purpose algorithms for tracking at large {eta} in order to increase muon acceptance. Upon analyzing the unblinded signal samples, I observe no X {yields} ZZ candidates and set upper limits on the production cross section using a Kaluza-Klein graviton-like acceptance.

This thesis describes a search for standard model Higgs bosons decaying to W boson pairs in proton-anti-proton collisions at a center of mass energy of 1.96 TeV using the CDF II detector. The decay to W bosons is dominant for Higgs masses greater than about 135 GeV. The final state examined consists of two leptons and missing transverse energy from the leptonic decay of one or more W bosons. The signal production mechanisms included are gluon fusion, associated production with a W or Z boson, and vector boson fusion. Matrix element calculations and artificial neural networks are used to discriminate signal from background for Higgs masses in the range 110 {le} M{sub H} {le} 200 GeV. No significant excess of events is observed at any of the Higgs masses investigated. Upper limits on the standard model Higgs cross section are set at 95% confidence for each Higgs mass investigated, the most stringent limit being 1.63 times the predicted standard model cross section for a Higgs mass of 160 GeV.

We present a search for a narrow resonance in the t{bar b} mass spectrum using 1.9 fb{sup -1} of p{bar p} collisions at {radical}s = 1.96 TeV recorded with the CDF II detector at the Fermilab Tevatron. We select events with a lepton, neutrino candidate, and two or three jets from which to construct the t{bar b} mass. We quantify the result using the model of a massive Standard Model-like charged-boson (W{prime}) decaying to t{bar b}, but we are generally sensitive to the presence of any narrow state decaying to the third generation. For a purely right-handed W{prime} with Standard Model couplings, we set a new limit at 95% confidence of {sigma}(p{bar p} {yields} W{prime}{sub R}) x BR(W{prime}{sub R} {yields} t{bar b}) < 0.28 pb and M{sub W{prime}{sub R}} > 800 GeV/c{sup 2}. The limit increases to M{sub W{prime}{sub R}} > 825 GeV/c{sup 2} if decay to right-handed neutrinos is forbidden. These results are shown in Table 7 and plotted in Figure 7.1. The best prior search found M{sub W{prime}} {ge} 768 GeV/c{sup 2} if leptonic decays are forbidden [16]. For a simple W{prime} model with effective coupling g{sub W{prime}}, the cross-section is proportional to g{sub W{prime}}{sup 4}. Relaxing the …